[gmx-users] Unexpected behavior of g_msd

[Darrell Koskinen]

Hi Berk, Yes, I am aware of the -b and -e options in g_msd but was 
wondering why the output said "Fitting from 4 to 35.9 ps" when I 
selected the time period from 60 to 100 ps. It appears that the output 
comment actually meant that it was fitting from 60+4 to 60+35.9 ps, but 
this is not clear to the user. At least, it was not obvious to me. When 
you say "MSD is a function of a time difference, not of simulation 
time", so you mean that I do not need to simulate for a longer period of 
time to get accurate results? Do I simply need to change trestart to a 
smaller value? Or is there something else I must do? Thanks. Darrell 
Date: Thu, 26 Nov 2009 10:27:27 +0100 From: Berk Hess <gmx3 at hotmail.com> 
Subject: RE: [gmx-users] Unexpected behavior of g_msd To: Discussion 
list for GROMACS users <gmx-users at gromacs.org> Message-ID: 
<COL113-W13EFECFADFB96DB6D2356B8E9B0 at phx.gbl> Content-Type: text/plain; 
charset="iso-8859-1" Hi, You don't need trjconv, g_msd has options -b 
and -e. But the regression is obviously done on the time differences and 
not on the frame times. MSD is a function of a time difference, not of 
simulation time. Berk

> > Date: Thu, 26 Nov 2009 13:24:12 +1100
> > From: Dallas.Warren at pharm.monash.edu.au
> > Subject: RE: [gmx-users] Unexpected behavior of g_msd
> > To: gmx-users at gromacs.org
> > 
> > trjconv
> > 
> > Catch ya,
> > 
> > Dr. Dallas Warren
> > Drug Delivery, Disposition and Dynamics
> > Monash Institute of Pharmaceutical Sciences, Monash University
> > 381 Royal Parade, Parkville VIC 3010
> > dallas.warren at pharm.monash.edu.au
> > +61 3 9903 9167
> > ---------------------------------
> > When the only tool you own is a hammer, every problem begins to resemble
> > a nail. 
> > 
> > 
>   
>> > > -----Original Message-----
>> > > From: gmx-users-bounces at gromacs.org [mailto:gmx-users-
>> > > bounces at gromacs.org] On Behalf Of Darrell Koskinen
>> > > Sent: Thursday, 26 November 2009 12:48 PM
>> > > To: gmx-users at gromacs.org
>> > > Subject: [gmx-users] Unexpected behavior of g_msd
>> > > 
>> > > Hi Tsjerk,
>> > > I looked at the .trr file and cannot read this file and simply delete
>> > > lines to create a sub-trajectory. So, how do I create a sub-trajectory
>> > > to analyze?
>> > > 
>> > > Thanks.
>> > > 
>> > > Darrell
>> > > 
>> > > Date: Wed, 25 Nov 2009 09:04:01 +0100 From: Tsjerk Wassenaar
>> > > <tsjerkw at gmail.com> Subject: Re: [gmx-users] Unexpected behavior of
>> > > g_msd To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> > > Message-ID:
>> > > <8ff898150911250004l42fee014qf3298816c9ef3db3 at mail.gmail.com>
>> > > Content-Type: text/plain; charset=ISO-8859-1 Hi Darrell, You can check
>> > > whether the output is identical to a trajectory of the specified
>> > > frames... It may well be that the counting for the regression is done
>> > > on
>> > > the frames read: 100 - 60 = 40 ps Then 4 and 35.9 would correspond to
>> > > 64
>> > > and 95.9. The answer is in the code... But using a subtrajectory may
>> > > give you good hint. Hope it helps, Tsjerk On Wed, Nov 25, 2009 at 7:42
>> > > AM, Darrell Koskinen <darrellk at ece.ubc.ca> wrote:
>> > > 
>>     
>>>> > > > > Dear GROMACS-ites,
>>>> > > > > I am a little confused by the behavior of g_msd. I have a trr file
>>>>         
>> > > with data
>>     
>>>> > > > > points from t=0 to t=100 ps and thought that the following command
>>>>         
>> > > would
>>     
>>>> > > > > perform a regression for the data points between t=60 ps and t=100
>>>>         
>> > > ps to
>>     
>>>> > > > > determine the diffision constant of the ammonia gas in the
>>>>         
>> > > simualtion:
>>     
>>>> > > > >
>>>> > > > > *g_msd -f mdtraj.trr -s mdtopol.tpr -type x -b 60 -e 100*
>>>> > > > >
>>>> > > > > However, the output:
>>>> > > > > *
>>>> > > > > /trn version: GMX_trn_file (single precision)
>>>> > > > > Reading frame     900 time   90.000
>>>> > > > >
>>>> > > > > Used 4 restart points spaced 10 ps over 39.9 ps
>>>> > > > >
>>>> > > > > Fitting from 4 to 35.9 ps
>>>> > > > >
>>>> > > > > D[       NH3] 3625.5647 (+/- 2802.0500) 1e-5 cm2/s
>>>> > > > > /*
>>>> > > > > seems to indicate that the regression was performed between t=4 ps
>>>>         
>> > > and
>>     
>>>> > > > > t=35.9 ps.
>>>> > > > >
>>>> > > > > Could you please explain to me what is happening?
>>>> > > > >
>>>> > > > > Thanks.
>>>> > > > >
>>>> > > > > Darrell
>>>>